Package org.biojava.nbio.core.sequence.io.embl

Class EmblRecord

  • public class EmblRecord
extends Object
    this class contains the parsed data of embl file
    Since:
    5.0.0
    Author:
    Noor Aldeen Al Mbaidin

    • Constructor Detail

      • EmblRecord

        public EmblRecord()

    • Method Detail

      • getEmblId

        public EmblId getEmblId()
        The ID (IDentification) line The tokens represent: 1. Primary accession number 2. Sequence version number 3. Topology: 'circular' or 'linear' 4. Molecule type 5. Data class 6. Taxonomic division 7. Sequence length
        Returns:
        EmblId

      • setEmblId

        public void setEmblId​(EmblId emblId)

      • getEmblReference

        public List<EmblReference> getEmblReference()
        The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines These lines comprise the literature citations within the database. The citations provide access to the papers from which the data has been abstracted.
        Returns:
        EmblReference

      • setEmblReference

        public void setEmblReference​(List<EmblReference> emblReference)

      • getAccessionNumber

        public List<String> getAccessionNumber()
        The AC (Accession number) line lists the accession numbers associated with the entry.
        Returns:
        List

      • setAccessionNumber

        public void setAccessionNumber​(List<String> accessionNumber)

      • getProjectIdentifier

        public String getProjectIdentifier()
        Returns:
        String

      • setProjectIdentifier

        public void setProjectIdentifier​(String projectIdentifier)

      • getOrGanelle

        public String getOrGanelle()
        The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.
        Returns:
        String

      • setOrGanelle

        public void setOrGanelle​(String orGanelle)

      • getCreatedDate

        public String getCreatedDate()
        The DT line shows when an entry first appeared in the database
        Returns:
        String

      • setCreatedDate

        public void setCreatedDate​(String createdDate)

      • getFeatureHeader

        public String getFeatureHeader()
        The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen.
        Returns:
        String

      • setFeatureHeader

        public void setFeatureHeader​(String featureHeader)

      • getFeatureTable

        public String getFeatureTable()
        The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data. Regions or sites in the sequence which are of interest are listed in the table.
        Returns:
        String

      • setFeatureTable

        public void setFeatureTable​(String featureTable)

      • getLastUpdatedDate

        public String getLastUpdatedDate()
        The DT (DaTe) line shows when an entry was last updated in the database.
        Returns:
        String

      • setLastUpdatedDate

        public void setLastUpdatedDate​(String lastUpdatedDate)

      • getSequenceDescription

        public String getSequenceDescription()
        The DE (Description) lines contain general descriptive information about the sequence stored. This may include the designations of genes for which the sequence codes, the region of the genome from which it is derived, or other information which helps to identify the sequence.
        Returns:
        String

      • setSequenceDescription

        public void setSequenceDescription​(String sequenceDescription)

      • getKeyword

        public List<String> getKeyword()
        The KW (KeyWord) lines provide information which can be used to generate cross-reference indexes of the sequence entries based on functional, structural, or other categories deemed important.
        Returns:
        List

      • setKeyword

        public void setKeyword​(List<String> keyword)

      • getOrganismSpecies

        public String getOrganismSpecies()
        The OS (Organism Species) line specifies the preferred scientific name of the organism which was the source of the stored sequence. In most cases this is done by giving the Latin genus and species designations, followed (in parentheses) by the preferred common name in English where known.
        Returns:
        String

      • setOrganismSpecies

        public void setOrganismSpecies​(String organismSpecies)

      • getOrganismClassification

        public String getOrganismClassification()
        The OC (Organism Classification) lines contain the taxonomic classification Of the source organism
        Returns:
        String

      • setOrganismClassification

        public void setOrganismClassification​(String organismClassification)

      • getDatabaseCrossReference

        public String getDatabaseCrossReference()
        The DR (Database Cross-reference) line cross-references other databases which contain information related to the entry in which the DR line appears.
        Returns:
        String

      • setDatabaseCrossReference

        public void setDatabaseCrossReference​(String databaseCrossReference)

      • getAssemblyHeader

        public String getAssemblyHeader()
        The AH (Assembly Header) line provides column headings for the assembly information.
        Returns:
        String

      • setAssemblyHeader

        public void setAssemblyHeader​(String assemblyHeader)

      • getAssemblyInformation

        public String getAssemblyInformation()
        The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.
        Returns:
        String

      • setAssemblyInformation

        public void setAssemblyInformation​(String assemblyInformation)

      • getConstructedSequence

        public String getConstructedSequence()
        Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.
        Returns:
        String

      • setConstructedSequence

        public void setConstructedSequence​(String constructedSequence)

      • getSequenceHeader

        public String getSequenceHeader()
        The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.
        Returns:
        String

      • setSequenceHeader

        public void setSequenceHeader​(String sequenceHeader)

      • getSequence

        public String getSequence()
        The Sequence Data Line
        Returns:
        String

      • setSequence

        public void setSequence​(String sequence)